estFragmentLength {ChIPpeakAnno} | R Documentation |
estimate the fragment length for bam files
estFragmentLength(bamfiles, index = bamfiles, plot = TRUE, lag.max = 1000, minFragmentSize=100, ...)
bamfiles |
The file names of the 'BAM' ('SAM' for asBam) files to be processed. |
index |
The names of the index file of the 'BAM' file being processed; this is given without the '.bai' extension. |
plot |
logical. If TRUE (the default) the acf is plotted. |
lag.max |
maximum lag at which to calculate the acf. See |
minFragmentSize |
minimal fragment size to avoid the phantom peak. |
... |
Not used. |
numberic vector
Jianhong Ou
if(Sys.getenv("USER")=="jianhongou"){ path <- system.file("extdata", "reads", package="MMDiffBamSubset") if(file.exists(path)){ WT.AB2 <- file.path(path, "WT_2.bam") Null.AB2 <- file.path(path, "Null_2.bam") Resc.AB2 <- file.path(path, "Resc_2.bam") estFragmentLength(c(WT.AB2, Null.AB2, Resc.AB2)) } }